I just investigated a similar case that happened to one of my beta testers. I took a look at his rom only to learn that his front sprite table was completely obliterated. This seems to confirm my theory that another program is accessing the rom at the same time and there is some corruption between programs. This issue is not at all related to filling with free space.
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Omg, I just realized: when some programs open roms, they copy the rom into the ram, do work, and then save back to the original. So, if you follow where I am going, that means that if you make changes in G3HS while the rom is open in another program, that ram copy may not get your changes and therefore will still see free space where you have just inserted data. Thus, when it saves, it thinks it can put data there and does so, overwriting your changes.
